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| author | mmonsoor |
|---|---|
| date | Tue, 24 Nov 2015 06:06:30 -0500 |
| parents | 054e4681667c |
| children | 588b0a7ae4b0 |
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<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> <requirements> <requirement type="package" version="3.1.2">R</requirement> <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.44.0">xcms</requirement> <requirement type="package" version="2.1">xcms_w4m_script</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <command> xcms.r #if $inputs.input == "lib": library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library #elif $inputs.input == "zip_file": zipfile $inputs.zip_file #end if xfunction xcmsSet ## profmethod $profmethod nSlaves \${GALAXY_SLOTS:-1} method $methods.method #if $methods.method == "centWave": ppm $methods.ppm peakwidth "c($methods.peakwidth)" #if $methods.options_scanrange.option == "show": scanrange "c($methods.options_scanrange.scanrange)" #end if #if $methods.options_c.option == "show": mzdiff $methods.options_c.mzdiff snthresh $methods.options_c.snthresh integrate $methods.options_c.integrate noise $methods.options_c.noise prefilter "c($methods.options_c.prefilter)" #end if #elif $methods.method == "matchedFilter": step $methods.step fwhm $methods.fwhm #if $methods.options_m.option == "show": ## sigma "$methods.options_m.sigma" max $methods.options_m.max snthresh $methods.options_m.snthresh ## mzdiff $methods.options_m.mzdiff steps $methods.options_m.steps ## sleep $methods.options_m.sleep #end if #elif $methods.method == "MSW": snthr $methods.snthr nearbyPeak $methods.nearbyPeak winSize.noise $methods.winSize_noise amp.Th $methods.amp_Th scales "c($methods.scales)" SNR.method "$methods.SNR_method" #end if && (mv xcmsSet.RData $xsetRData; mv sampleMetadata.tsv $sampleMetadata; mv TICs_raw.pdf $ticsRawPdf; mv BPCs_raw.pdf $bpcsRawPdf; mv xset.log $log); cat $log </command> <inputs> <conditional name="inputs"> <param name="input" type="select" label="Choose your inputs method" > <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> <option value="lib" >Library directory name</option> </param> <when value="zip_file"> <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> </when> <when value="lib"> <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > <validator type="empty_field"/> </param> </when> </conditional> <!-- <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" > <option value="bin" selected="true">bin</option> <option value="binlin">binlin</option> <option value="binlinbase">binlinbase</option> <option value="intlin">intlin</option> </param> <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" /> --> <conditional name="methods"> <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below"> <option value="centWave" >centWave</option> <option value="matchedFilter" selected="true">matchedFilter</option> <option value="MSW">MSW</option> </param> <!-- centWave Filter options --> <when value="centWave"> <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" /> <conditional name="options_scanrange"> <param name="option" type="select" label="Scan range option " > <option value="show">show</option> <option value="hide" selected="true">hide</option> </param> <when value="show"> <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" > <validator type="empty_field"/> </param> </when> </conditional> <conditional name="options_c"> <param name="option" type="select" label="Advanced options" > <option value="show">show</option> <option value="hide" selected="true">hide</option> </param> <when value="show"> <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " /> <param name="integrate" type="select" label="peak limits method" help="[integrate]" > <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> <option value="2">peak limits based on real data (more sensitive to noise)</option> </param> <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> </when> </conditional> </when> <!-- matched Filter options --> <when value="matchedFilter"> <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> <conditional name="options_m"> <param name="option" type="select" label="Advanced options" > <option value="show">show</option> <option value="hide" selected="true">hide</option> </param> <when value="show"> <!-- <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" /> --> <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> <!-- <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " /> --> </when> </conditional> </when> <!-- MSW Filter options --> <when value="MSW"> <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" > <option value="TRUE">TRUE</option> <option value="FALSE">FALSE</option> </param> <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" /> <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" /> <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" /> <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " /> <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." /> </when> </conditional> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" /> <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" /> <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" /> <data name="log" format="txt" label="xset.log.txt" /> </outputs> <tests> <test> <param name="inputs.input" value="zip_file" /> <param name="inputs.zip_file" value="sacuri.zip" /> <param name="methods.method" value="matchedFilter" /> <param name="methods.step" value="0.01" /> <param name="methods.fwhm" value="4" /> <param name="methods.options_m.option" value="show" /> <param name="methods.options_m.max" value="50" /> <param name="methods.options_m.snthresh" value="1" /> <param name="methods.options_m.steps" value="2" /> <output name="xsetRData" file="xset.RData" /> <output name="sampleMetadata" file="sampleMetadata.tsv" /> <output name="ticsRawPdf" file="xset.TICs_raw.pdf" /> <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" /> <output name="log" file="xset.log.txt" /> </test> </tests> <help> .. class:: infomark **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu .. class:: infomark **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. --------------------------------------------------- ============ Xcms.xcmsSet ============ ----------- Description ----------- This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated. You can read a tutorial on how to perform xcms preprocessing which is available here_. .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf ----------------- Workflow position ----------------- **Upstream tools** ========================= ================= ======= ========= Name output file format parameter ========================= ================= ======= ========= NA NA zip NA ========================= ================= ======= ========= **Downstream tools** +---------------------------+--------------------+-----------------+ | Name | Output file | Format | +===========================+====================+=================+ |xcms.group | xset.RData | rdata.xcms.raw | +---------------------------+--------------------+-----------------+ |PCA ellipsoid by factors | sampleMetadata.tsv | Tabular | +---------------------------+--------------------+-----------------+ |Anova | sampleMetadata.tsv | Tabular | +---------------------------+--------------------+-----------------+ **Example of a metabolomic workflow** .. image:: XCMS_Galaxy_workflow.png ------ .. class:: infomark The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. --------------------------------------------------- ----------- Input files ----------- +---------------------------+------------+ | Parameter : num + label | Format | +===========================+============+ | 1 : Choose your inputs | zip | +---------------------------+------------+ **Choose your inputs** You have two methods for your inputs: | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. ---------- Parameters ---------- Extraction method for peaks detection ------------------------------------- **Matched Filter** | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002). **cent Wave** | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode. | Due to the fact that peak centroids are used, a binning step is not necessary. | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals. **MSW** | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales. | If you wish to have more details about the other parameters, you can read the following documents: | -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf | -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf ------------ Output files ------------ xset.TICs_raw.pdf | "Total Ion Chromatograms" graph in pdf format. xset.BPCs_raw.pdf | "Base Peak Chromatograms" graph in pdf format with each class samples opposed. sampleMetadata.tsv | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed). | This file is necessary in the Anova and PCA step of the workflow. xset.RData: rdata.xcms.raw format | Rdata file that is necessary in the second step of the workflow "xcms.group". ------ .. class:: infomark The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. --------------------------------------------------- --------------- Working example --------------- Input files ----------- | zip_file -> **sacuri.zip** Parameters ---------- | Method -> **matchedFilter** | step -> **0.01** | fwhm -> **4** | Advanced option -> **show** | max: -> **50** | snthresh -> **1** | steps -> **2** Output files ------------ | **1) xset.RData: RData file** | **2) Example of a sampleMetadata.tsv :** +---------------------------+------------+---------+ | sampleMetadata | class | polarity| +===========================+============+=========+ |HU_neg_017 | bio |negative | +---------------------------+------------+---------+ |HU_neg_028 | bio |negative | +---------------------------+------------+---------+ |HU_neg_034 | bio |negative | +---------------------------+------------+---------+ |Blanc04 | blank |negative | +---------------------------+------------+---------+ |Blanc06 | blank |negative | +---------------------------+------------+---------+ |Blanc09 | blank |negative | +---------------------------+------------+---------+ | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :** .. image:: xcms_tics.png </help> <citations> <citation type="doi">10.1021/ac051437y</citation> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </tool>